PrimerPlex

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Oligo Design for High Throughput SNP Genotyping, SNP Analysis & More...

PrimerPlex is an efficient and sophisticated tool for designing multiplex oligos for multiplex analysis platforms such as Luminex 100, Luminex 200, Bio-Plex 200 suspension array systems. Based on Luminex Corporation’s xMAP® technology, these systems offer a versatile platform for multiplex nucleic acid detection in a 96-well format.

PrimerPlex designs specific capture probes for direct hybridization assays and primers for Allele Specific PCR Extension (ASPE), for multiplexed high throughput SNP genotyping applications such as SNP analysis, pathogen detection, strain typing, and haplotyping. The oligos are designed after avoiding the regions of homology identified by a BLAST search.

PrimerPlex checks the oligos for cross homologies and minimizes Tm mismatches to give you the best possible multiplex set. In the process, it analyzes millions of possible multiplex sets in a flash. In addition, PrimerPlex presents a list of alternate sets for you to choose from, based on your specific experimental needs.

Design Options

Direct Hybridization Assays:

PrimerPlex designs optimal allele specific capture probes for direct hybridization assays. The probes are designed such that the SNPs are at their centers. Our innovative and proprietary algorithm analyzes each of these probes for their suitability in a multiplex reaction. The probes are screened for cross and self dimers, assuring strong signal strength.

This functionality makes PrimerPlex the only software product capable of designing probes for 100 individual targets in a single tube multiplex reaction. Also included is the ability to design compatible primer pairs for amplifying the template.

A series of probes can also be designed for detecting variable sites of a particular gene. For such cases, PrimerPlex designs equal length capture probes after BLAST searching the sequences and avoiding the regions of homology.

ASPE Assays:

Another approach to detect SNPs is to use a solution-based sequence specific enzymatic reaction such as ASPE to determine the target genotype.

PrimerPlex designs highly specific primers for multiplexed ASPE assays. The ASPE primers are designed such that the SNP lies at their 3' end.

PrimerPlex also designs primers to amplify the target sequence for ASPE assays. The primers could be designed for a multiplexed reaction as well.